def test_repo_training_test_data(self):
# init repository with sample in memory handler
repository = MLRepo(user='******')
job_runner = SimpleJobRunner(repository)
repository._job_runner = job_runner
training_data = RawData(
np.zeros([10, 1]), ['x_values'],
np.zeros([10, 1]), ['y_values'],
repo_info={repo_objects.RepoInfoKey.NAME.value: 'training_data'})
repository.add(training_data, category=MLObjectType.TRAINING_DATA)
training_data_2 = repository.get_training_data()
self.assertEqual(
training_data_2.repo_info[repo_objects.RepoInfoKey.NAME],
training_data.repo_info[repo_objects.RepoInfoKey.NAME])
test_data = RawData(
np.zeros([10, 1]), ['x_values'],
np.zeros([10, 1]), ['y_values'],
repo_info={repo_objects.RepoInfoKey.NAME.value: 'test_data'})
repository.add(test_data, category=MLObjectType.TEST_DATA)
test_data_ref = repository.get('test_data')
self.assertEqual(
test_data_ref.repo_info[repo_objects.RepoInfoKey.NAME],
test_data.repo_info[repo_objects.RepoInfoKey.NAME])
self.assertEqual(
test_data_ref.repo_info[repo_objects.RepoInfoKey.VERSION],
test_data.repo_info[repo_objects.RepoInfoKey.VERSION])
test_data_2 = RawData(
np.zeros([10, 1]), ['x_values'],
np.zeros([10, 1]), ['y_values'],
repo_info={repo_objects.RepoInfoKey.NAME.value: 'test_data_2'})
repository.add(test_data_2, category=MLObjectType.TEST_DATA)
test_data_2_ref = repository.get('test_data_2')
self.assertEqual(
test_data_2.repo_info[repo_objects.RepoInfoKey.NAME],
test_data_2_ref.repo_info[repo_objects.RepoInfoKey.NAME])
commits = repository.get_commits()
self.assertEqual(len(commits), 3)
self.assertEqual(commits[1].objects['test_data'],
test_data.repo_info.version)
#self.assertEqual(commits[1].objects['repo_mapping'], 1)
self.assertEqual(commits[2].objects['test_data_2'],
test_data_2.repo_info.version)
def test_repo_RawData(self):
"""Test RawData within repo
"""
repository = MLRepo(user='******')
job_runner = SimpleJobRunner(repository)
repository._job_runner = job_runner
raw_data = repo_objects.RawData(
np.zeros([10, 1]),
['test_coord'],
repo_info={ # pylint: disable=E0602
repo_objects.RepoInfoKey.NAME.value: 'RawData_Test'
})
repository.add(raw_data, 'test commit', MLObjectType.RAW_DATA)
raw_data_2 = repository.get('RawData_Test')
self.assertEqual(len(raw_data.x_coord_names),
len(raw_data_2.x_coord_names))
self.assertEqual(raw_data.x_coord_names[0],
raw_data_2.x_coord_names[0])
commits = repository.get_commits()
self.assertEqual(len(commits), 1)
self.assertEqual(len(commits[0].objects), 1)
def test_tutorial(self):
# cleanup disk before running
repo_path = './tmp_tutorial'
try:
shutil.rmtree(repo_path)
# os.path.
except OSError:
pass
# creating in memory storage
ml_repo = MLRepo(user='******')
# end creating in memory storage
# creating new repository
config = {'user': '******',
'workspace': repo_path,
'repo_store':
{
'type': 'disk_handler',
'config': {
'folder': repo_path,
'file_format': 'pickle'
}
},
'numpy_store':
{
'type': 'hdf_handler',
'config': {
'folder': repo_path,
'version_files': True
}
},
'job_runner':
{
'type': 'simple',
'config': {
'throw_job_error': True
}
}
}
ml_repo = MLRepo(user='******', config=config)
# end creating new repository
# specifying job runner
job_runner = SimpleJobRunner(None)
job_runner.set_repo(ml_repo)
ml_repo._job_runner = job_runner
# end specifying job runner
job_runner._throw_job_error = True
from pailab.tools.tree import MLTree
MLTree.add_tree(ml_repo)
# A convenient way to add RawData is simply to use the method add on the raw_data collection.
# This method just takes a pandas dataframe and the specification, which columns belong to the input
# and which to the targets.
try:
# read pandas
import pandas as pd
data = pd.read_csv('./examples/boston_housing/housing.csv')
# end read pandas
except:
data = pd.read_csv('../examples/boston_housing/housing.csv')
# extract data
input_variables = ['RM', 'LSTAT', 'PTRATIO']
target_variables = ['MEDV']
x = data.loc[:, input_variables].values
y = data.loc[:, target_variables].values
# end extract data
# add RawData snippet
from pailab import RawData, RepoInfoKey
raw_data = RawData(x, input_variables, y, target_variables, repo_info={
RepoInfoKey.NAME: 'raw_data/boston_housing'})
ml_repo.add(raw_data)
# end adding RawData snippet
# ml_repo.tree.raw_data.add('boston_housing', data, input_variables=[
# 'RM', 'LSTAT', 'PTRATIO'], target_variables=['MEDV'])
# add DataSet
# create DataSet objects for training and test data
training_data = DataSet('raw_data/boston_housing', 0, 300,
repo_info={RepoInfoKey.NAME: 'training_data', RepoInfoKey.CATEGORY: MLObjectType.TRAINING_DATA})
test_data = DataSet('raw_data/boston_housing', 301, None,
repo_info={RepoInfoKey.NAME: 'test_data', RepoInfoKey.CATEGORY: MLObjectType.TEST_DATA})
# add the objects to the repository
version_list = ml_repo.add(
[training_data, test_data], message='add training and test data')
# end adding DataSet
# add model
import pailab.externals.sklearn_interface as sklearn_interface
from sklearn.tree import DecisionTreeRegressor
sklearn_interface.add_model(
ml_repo, DecisionTreeRegressor(), model_param={'max_depth': 5})
# end adding model
# run training
job_id = ml_repo.run_training()
# end running training
# run evaluation
job_id = ml_repo.run_evaluation()
# end running evaluation
# add measures snippet
ml_repo.add_measure(MeasureConfiguration.MAX)
ml_repo.add_measure(MeasureConfiguration.R2)
# end add measure snippet
# run measures snippet
job_ids = ml_repo.run_measures()
# end run measures snippet
print(ml_repo.get_names(MLObjectType.MEASURE))
# get measures
max_measure = ml_repo.get(
'DecisionTreeRegressor/measure/training_data/max')
print(str(max_measure.value))
# end getting measures
# label snippet
from pailab import LAST_VERSION
ml_repo.set_label('prod', 'DecisionTreeRegressor/model',
model_version=LAST_VERSION, message='we found our first production model')
# end label snippet
# test definition snippet
import pailab.tools.tests
reg_test = pailab.tools.tests.RegressionTestDefinition(
reference='prod', models=None, data=None, labels=None,
measures=[MeasureConfiguration.MAX], tol=1000)
reg_test.repo_info.name = 'reg_test'
ml_repo.add(reg_test, message='regression test definition')
# end test definition snippet
# add test snippet
tests = ml_repo.run_tests()
# end add test snippet
print(tests)
# run check snippet
import pailab.tools.checker as checker
inconsistencies = checker.run(ml_repo)
# end run check snippet
print(inconsistencies)
# add inconsistency snippet
param = ml_repo.get('DecisionTreeRegressor/model_param')
param.sklearn_params['max_depth'] = 2
version = ml_repo.add(param)
# end add inconsistency snippet
inconsistencies = checker.run(ml_repo)
print(inconsistencies)
ml_repo.run_training()
inconsistencies = checker.run(ml_repo)
print(inconsistencies)
ml_repo.run_evaluation(run_descendants=True)
print(checker.run(ml_repo))
# add second test data snippet
test_data_2 = DataSet('raw_data/boston_housing', 0, 50,
repo_info={RepoInfoKey.NAME: 'test_data_2',
RepoInfoKey.CATEGORY: MLObjectType.TEST_DATA}
)
ml_repo.add(test_data_2)
ml_repo.run_evaluation(run_descendants=True)
# end add second test data snippet
print(checker.Tests.run(ml_repo))
ml_repo.run_tests()
# check tests
print(checker.Tests.run(ml_repo))
# end check tests
# cleanup after running
# job_runner.close_connection()
ml_repo._ml_repo.close_connection()
try:
shutil.rmtree(repo_path)
# os.path.
except OSError:
pass
